[2024-01-24 11:51:50,471] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg339fc1fb-17d2-4b24-9722-fa7a1a39c88a/dqc_reference
[2024-01-24 11:51:51,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,686] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg211f3765-368c-460b-99b0-010c05680b83/GCF_008039565.1_ASM803956v1_genomic.fna.gz | prodigal -d GCF_008039565.1_ASM803956v1_genomic.fna/cds.fna -a GCF_008039565.1_ASM803956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:00,441] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:00,442] [INFO] Task started: HMMsearch
[2024-01-24 11:52:00,442] [INFO] Running command: hmmsearch --tblout GCF_008039565.1_ASM803956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg339fc1fb-17d2-4b24-9722-fa7a1a39c88a/dqc_reference/reference_markers.hmm GCF_008039565.1_ASM803956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:00,680] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:00,681] [INFO] Found 6/6 markers.
[2024-01-24 11:52:00,713] [INFO] Query marker FASTA was written to GCF_008039565.1_ASM803956v1_genomic.fna/markers.fasta
[2024-01-24 11:52:00,713] [INFO] Task started: Blastn
[2024-01-24 11:52:00,714] [INFO] Running command: blastn -query GCF_008039565.1_ASM803956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg339fc1fb-17d2-4b24-9722-fa7a1a39c88a/dqc_reference/reference_markers.fasta -out GCF_008039565.1_ASM803956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:01,957] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:01,961] [INFO] Selected 16 target genomes.
[2024-01-24 11:52:01,961] [INFO] Target genome list was writen to GCF_008039565.1_ASM803956v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:02,031] [INFO] Task started: fastANI
[2024-01-24 11:52:02,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg211f3765-368c-460b-99b0-010c05680b83/GCF_008039565.1_ASM803956v1_genomic.fna.gz --refList GCF_008039565.1_ASM803956v1_genomic.fna/target_genomes.txt --output GCF_008039565.1_ASM803956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:14,464] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:14,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg339fc1fb-17d2-4b24-9722-fa7a1a39c88a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:14,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg339fc1fb-17d2-4b24-9722-fa7a1a39c88a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:14,480] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:14,480] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:14,481] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	100.0	1039	1039	95	conclusive
Aeromicrobium erythreum	strain=AR18	GCA_001509405.1	2041	2041	type	True	81.1927	575	1039	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	81.1324	604	1039	95	below_threshold
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	80.9834	636	1039	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	80.8924	589	1039	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	80.8563	573	1039	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	80.7771	606	1039	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	80.6844	545	1039	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	80.6372	494	1039	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	80.5735	498	1039	95	below_threshold
Aeromicrobium marinum	strain=DSM 15272	GCA_000160775.2	219314	219314	type	True	80.3896	517	1039	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	78.7495	435	1039	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.7072	445	1039	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	78.4816	399	1039	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	78.4615	454	1039	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	78.3646	402	1039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:14,484] [INFO] DFAST Taxonomy check result was written to GCF_008039565.1_ASM803956v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:14,485] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:14,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:14,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg339fc1fb-17d2-4b24-9722-fa7a1a39c88a/dqc_reference/checkm_data
[2024-01-24 11:52:14,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:14,524] [INFO] Task started: CheckM
[2024-01-24 11:52:14,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008039565.1_ASM803956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008039565.1_ASM803956v1_genomic.fna/checkm_input GCF_008039565.1_ASM803956v1_genomic.fna/checkm_result
[2024-01-24 11:52:58,465] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:58,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:58,488] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:58,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:58,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008039565.1_ASM803956v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:58,490] [INFO] Task started: Blastn
[2024-01-24 11:52:58,490] [INFO] Running command: blastn -query GCF_008039565.1_ASM803956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg339fc1fb-17d2-4b24-9722-fa7a1a39c88a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008039565.1_ASM803956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:00,499] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:00,503] [INFO] Selected 14 target genomes.
[2024-01-24 11:53:00,504] [INFO] Target genome list was writen to GCF_008039565.1_ASM803956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:00,532] [INFO] Task started: fastANI
[2024-01-24 11:53:00,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg211f3765-368c-460b-99b0-010c05680b83/GCF_008039565.1_ASM803956v1_genomic.fna.gz --refList GCF_008039565.1_ASM803956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008039565.1_ASM803956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:11,857] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:11,879] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:11,879] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_008039565.1	s__Aeromicrobium terrae	100.0	1039	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014873655.1	s__Aeromicrobium sp014873655	92.5671	913	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428805.1	s__Aeromicrobium sp001428805	81.3794	639	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509405.1	s__Aeromicrobium erythreum	81.2172	573	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.57	98.39	0.93	0.92	6	-
GCF_001426485.1	s__Aeromicrobium sp001426485	81.1265	584	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.44	97.44	0.91	0.91	2	-
GCF_001423335.1	s__Aeromicrobium sp001423335	81.1232	575	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	98.72	97.77	0.96	0.93	5	-
GCF_004134905.2	s__Aeromicrobium ginsengisoli	80.9494	639	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000471045.1	s__Aeromicrobium sp000471045	80.8973	499	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586285.1	s__Aeromicrobium endophyticum	80.7772	606	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336805.1	s__Aeromicrobium sp004336805	80.762	531	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312105.1	s__Aeromicrobium massiliense	80.743	540	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013408555.1	s__Aeromicrobium tamlense	80.6534	492	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000160775.2	s__Aeromicrobium marinum	80.389	517	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729525.1	s__Nocardioides sp002729525	78.4998	423	1039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:11,881] [INFO] GTDB search result was written to GCF_008039565.1_ASM803956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:11,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:11,885] [INFO] DFAST_QC result json was written to GCF_008039565.1_ASM803956v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:11,885] [INFO] DFAST_QC completed!
[2024-01-24 11:53:11,886] [INFO] Total running time: 0h1m21s